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RNA structures (DSSR) / Re: Can 3DNA DSSR handle Left-handed DNA?

« on: Yesterday at 09:58:56 pm »

Dear Xiang-Jun,

I am currently using DSSR to help me figure out the base pair, step base pair, helical base pair parameters difference between D and L form B-DNA. I just notice this post is regarding L-form DNA recognition and realize you update DSSR in v2.7.1 to acommondate L-DNA is a sense while I am still using a bit outdated version DSSR v2.6.0-2025jul24 to analyze a native B-DNA duplex and its mirror-image counterpart.

Specifically, I used PDB entry 1BNA as the native structure and generated a mirror-image structure by reflecting the X coordinates(x -> -x). I attached the JSON format output file in this post, but anyway I list the sign inversion conclusion here:

Code: [Select]

Shear      : no sign inversion
Stretch    : no sign inversion
Stagger    : sign inversion
Buckle     : sign inversion
Propeller  : sign inversion
Opening    : no sign inversion

Code: [Select]

Shift  : no sign inversion
Slide  : sign inversion
Rise   : no sign inversion
Tilt   : sign inversion
Roll   : no sign inversion
Twist  : sign inversion

Code: [Select]

x-displacement : no sign inversion
y-displacement : sign inversion
helical rise   : no sign inversion
inclination    : sign inversion
tip            : no sign inversion
helical twist  : sign inversionHere which makes me feel confused is that the sign inversion pattern of the base pair parameters is different from that of the step and helical parameters. I understand that if the inversion pattern of bp parameters apply to step/helical bp parameter, such as Twist and Helical Twist will be "no sign inversion" which is impossible since the most distinct difference between native and mirror-image double helix is right and left handed. I looked into X3DNA and also SCHNAaP paper which has detailed description about how to calculate the parameters which makes believe the sign inversion pattern should be same . Probably DSSR has some certain axis direction inversion when calculate step/helical bp parameters which I overlooked.

I am also wondering the DSSR V2.7.1 or the newest version will give out the same conclusion or there is some certain adaption when encounter L-form when calculating the parameters. I will be very grateful to your help and sorry if I misunderstood something.